Friday, December 9, 2011

Independent Intron Insertion: More Evidence for Common Mechanism

It is perhaps the most celebrated evolutionary evidence from the genomics era. Like a grammar school teacher who knows cheating occurred when he sees identical typos in essays from different students, evolutionists know common descent occurred when they see identical junk DNA (yes we know the junk DNA often seems to be found to be functional, but that’s a different story) in the genomes of different species. In what philosopher Elliott Sober has called Modus Darwin, evolutionists reason that only evolution can account for these so-called shared errors. But is the premise true? Can only evolution account for such observations? (yes we know the evolutionary reasoning is, as usual, not scientific, but that’s a different story).

In fact sometimes these shared errors cannot be shared after all. Like identical typos in essays from students who have never met, sometimes the identical junk DNA could not have originated from a common ancestor even if one believed in the mythical common descent to begin with. In these cases evolutionists agree that lightning did strike twice, such as in this study which found introns at common DNA insertion sites. As one evolutionist put it:

Remarkably, we have found many cases of parallel intron gains at essentially the same sites in independent genotypes. This strongly argues against the common assumption that when two species share introns at the same site, it is always due to inheritance from a common ancestor.

What if common descent had been the only explanation for such similarities in the genomes of different species? That would have been remarkable given the substantial scientific problems with the idea.

That "one" evolutionist was none other than Michael Lynch. He leads the effort to come up with a viable population genetics approach for Darwinism. That he would say this evidence points away from common inheritance is quite significant.

"That "one" evolutionist was none other than Michael Lynch. He leads the effort to come up with a viable population genetics approach for Darwinism."

Not for "Darwinism" but for evolutionary genetics, which encompasses more than just Darwinian adaptive evolution. Lynch uses classical population genetic models of selection, mutation and drift to study evolution.

Lynch:

"A central point to be explored in this book [The Origins of Genome Architecture] is that most aspects of evolution at the genomic level cannot be fully explained in adaptive terms, and moreover, that many genomic features could not have emerged without a near-complete disengagement of the power of natural selection. This contention is supported by a wide array of comparative data, as well as by well-established principles of population genetics."

Lynch makes a big point of small population sizes of "higher" organisms causing selection to be relatively weak compared to drift, and that this is why genomes of higher organisms carry a lot of non-functional garbage around. Selection often isn't strong enough to get rid of it, because of the small population sizes.

The explanation presented for the insertion of the introns in question was a common DNA repair mechanism. Furthermore, the majority of these introns insertions are though to be deleterious.

More than half of the recent gains are associated with short sequence repeats, suggesting an origin via repair of staggered double-strand breaks. By comparing the allele-frequency spectrum of intron-gain alleles with that for derived single-base substitutions, we also provide evidence that newly arisen introns are intrinsically deleterious and tend to accumulate in population-genetic settings where random genetic drift is a relatively strong force.

1. Neither Mike Lynch, his research, nor a single member of his lab have the slightest shred of doubt that all known extant life shares a evolutionary common origin. Your quotemines are disingenuous and borderline libelous.

2. Lynch has nothing to do with Darwinism, Neo- or otherwise. In fact, few of us actually working in the field of evolutionary biology even care about Darwin's exact theory anymore (except from a history of science perspective). That would be analogous to a particle physicist obsessing over the wording of Newton's Principia. We have moved on as a science. Doesn't matter whether he was right or wrong anymore, as the sheer vastness of knowledge accumulated on the subject far exceeds a single individual.

3. You do not understand how phylogenetic analyses are done. It is not automatically assumed that a shared sequence is shared due to the common ancestor possessing that exact sequence -- in reality, a fairly complicated statistical toolkit exists to evaluate how likely it is that a sequence is similar or identical due to a shared ancestral form, *with respect to that particular sequence*. It may be that both my third cousin and I got the same silent (say, nonsensical) sequence insertion or mutation completely by chance -- and we probably do have a few, due to statistical chance -- but that doesn't then mean we are not related. However, given enough sequence data, it becomes more apparent that my mother is more closely related to me than said third cousin, even if that particular accidental short sequence speaks otherwise. These kinds of things are most definitely accounted for -- we're not stupid.

Furthermore, you seem to confuse non-coding intergenic space with introns -- understandably so as they're often both referred to as junk (a debate for another day). This is important due to difference in scale -- introns tend to be fairly short compared to other 'junk' DNA in the genome, and act as a class of their own as far as non-coding sequences go. They're not the same as pseudogenes, degraded transposons or tandem repeats. Do understand that the Daphnia intron gain example is a rare case -- it most likely happens from time to time in a variety of lineages, but rarely enough that it's gone undetected until the late 2000's, when this research was done. Actually, this leads me to my last point:

4. You did not understand the Daphnia intron gain paper, nor its significance. It's a nuanced and fairly technical field to begin with, and Science/Nature papers tend to be highly condensed and therefore hard to read, even to scientists; and press releases are oft inaccurate or confusing. That said, you would look a little bit less awkward if you genuinely attempted to comprehend the paper without plunging head-first into a morass of assumptions and accusations.

The authors sampled several Daphnia strains from a variety of locations, and found clear phylogenetic evidence not only for intron gain to begin with -- already an interesting and somewhat uncommon finding, perhaps in part due to paucity of population genetic analyses like this -- but for three *independent* instances thereof (tree in fig2). Furthermore, as the alignment in fig1 shows, these intron gains occured at the same site, indicating there's something special about that location, probably for a biochemical reason (more on that in a bit).

Of course, if you're wondering what this has to do with organisms adapting and getting 'better' -- very little at all. But then again, adaptation is but one aspect of evolution, and in fact an emergent property of heritable variation and selection. Besides selection, there's also phenomena like drift and mutation that shape the ever-changing lifeforms. Most mutations are indeed deleterious or effectively neutral (the latter category growing as populations shrink), and most selection is stabilising, ie maintaining the populations in the same place. Where selection is weakened due to reduced population size, for example, some of the population's traits are allowed to 'wander' more in parameter space, occasionally generating something that is either positively selected for, or, more often, ratcheted into being by its reversal being considerably less likely. In other words, adaptation is but one part of evolutionary theory.

These gained introns are in fact slightly deleterious, and stabilising selection is acting *against* them, as shown in the allele frequency spectrum in fig 3 (compared to presumably largely neutral single nucleotide changes, the frequency of derived introns is much lower -- they're rarer than you would expect if they were effectively neutral). So why, you may rightly wonder, are these introns allowed to exist in the first place, if they have no advantage to the organism? Incidentally, these gains occurred in lineages known to be afflicted by small population sizes, meaning drift is more likely to fix slightly-deleterious traits before selection gets around to weeding them out.

These intron gains included. As mentioned above, their origin was probably not due to any benefit to the organism (or any 'evolutionary' reason, so to speak, in common parlance), as clearly selection does not particularly care for them -- thus, we're satisfied with a neutral reason for them, which in this case appears to be a vulnerability of the site in question to double strand breaks (in the DNA). In most cases, this is repaired fine, we never see any intron and there's nothing to speak of. But in some cases, a bunch of junk gets inserted during the double stranded breakage repair. Again, in most of *those* cases, the junk disrupts the gene's function, the organism dies, we never get to speak of it since. But in some cases, this junk happens to have the right sequence at both ends to be recognised by a spliceosome -- the intron removal machine -- and act as a true, de novo intron. That only requires two correct nucleotides at either end, so the chances aren't all *that* low. Lastly, there are millions upon millions upon millions of Daphnias alive today, reproducing when only a week old, and every few days subsequently, until death. Point is, there's a crapload of Daphnia out there, and lots of opportunity for even somewhat rare changes to occur. And when they do occur, we notice them, so there's an observational bias there -- specifically in a study that specifically focuses on unusual intron gains.

Parallel (similar sequence, different origin) intron gain does NOT invalidate shared *organism* ancestry, and in fact *requires* shared organismal ancestry to even make basic sense.

Thank you for your detailed comment, however, you have made several false accusations. You have accused me of being presumptuous or ignorant of what I am commenting on, but that is precisely what you have done.

1. Neither Mike Lynch, his research, nor a single member of his lab have the slightest shred of doubt that all known extant life shares a evolutionary common origin. Your quotemines are disingenuous and borderline libelous.

That is quite a charge, particularly given that, aside from the bluster, it misrepresents the OP. Nowhere do I say (nor did I say in the OP) that Lynch doubts evolution.

2. Lynch has nothing to do with Darwinism, Neo- or otherwise. In fact, few of us actually working in the field of evolutionary biology even care about Darwin's exact theory anymore (except from a history of science perspective). That would be analogous to a particle physicist obsessing over the wording of Newton's Principia. We have moved on as a science. Doesn't matter whether he was right or wrong anymore, as the sheer vastness of knowledge accumulated on the subject far exceeds a single individual

This is an even more bizarre comment as I never said anything of the sort.

3. You do not understand how phylogenetic analyses are done. It is not automatically assumed that a shared sequence is shared due to the common ancestor possessing that exact sequence –

Yet another false accusation. I never said anything of the sort.

in reality, a fairly complicated statistical toolkit exists to evaluate how likely it is that a sequence is similar or identical due to a shared ancestral form, *with respect to that particular sequence*.

This is becoming embarrassing.

Furthermore, you seem to confuse non-coding intergenic space with introns

I never said otherwise. This is unfortunately a typical evolutionary response. A hypocritical misrepresentation full of false accusations from someone who believes all of biology arose spontaneously, on its own. And then this:

and in fact *requires* shared organismal ancestry to even make basic sense.

In fact, few of us actually working in the field of evolutionary biology even care about Darwin's exact theory anymore (except from a history of science perspective). That would be analogous to a particle physicist obsessing over the wording of Newton's Principia. We have moved on as a science. Doesn't matter whether he was right or wrong anymore, as the sheer vastness of knowledge accumulated on the subject far exceeds a single individual.

And, then, in [4] you said this:Of course, if you're wondering what this has to do with organisms adapting and getting 'better' -- very little at all. But then again, adaptation is but one aspect of evolution, and in fact an emergent property of heritable variation and selection. Besides selection, there's also phenomena like drift and mutation that shape the ever-changing lifeforms. Most mutations are indeed deleterious or effectively neutral (the latter category growing as populations shrink), and most selection is stabilising, ie maintaining the populations in the same place. Where selection is weakened due to reduced population size, for example, some of the population's traits are allowed to 'wander' more in parameter space, occasionally generating something that is either positively selected for, or, more often, ratcheted into being by its reversal being considerably less likely. In other words, adaptation is but one part of evolutionary theory.

From the highlighted phrase in [4], it's clear you belong to the "neutral drift" crowd. So, then, it's no matter then that you throw Darwin over the side of the boat, as you do in the highlighted sentence from [2] above.

But things aren't that simple are they?

If, as you say, selection is mostly stabilizing, then how is evolution driven forward? Only positive selection can overcome the tremendous time constraints of neutral drift. So how, exactly, did the genome arise? How does it change with time?

You might suggest small populations, where positive selection (in this case positive selection 'against' deleterious mutations) is constrained, leaving more room for nearly neutral mutations to exist; but, then this reduces the number of mutations that will be generated in any interval of time. And getting any specific mutation via neutral drift requires lots of generations. So this becomes problematic.

In the case of Daphnia, producing plenty of offspring and quickly reproducing, neutral drift can accomplish a fair amount. But can neutral drift tell us how a chimpanzee turned human in 10 to 20 million years?

I'm afraid that without Darwin, you're assuming an evolutionary power without ever having demonstrated its power to exist. This, too, is problematic.

As to the double-stranded breaks, you say that Daphnia is susceptible to these. You say that as a Darwinist (evolutionary geneticist). As someone who has no faith at all in Darwinian mechanisms for explaining evolution, and who puts his weight behind ID as a plausible, sensible explanation, I see it differently.

So, let me, from an ID perspective, predict something. I predict that it will be established that Daphnia, and related organism, USE double-stranded breaks, with the concomitant random generation of nucleotide strings, to overcome environmental challenges. That is, the DB breaks are simply a built-in mechanism, a strategy employed by the organisms, to adapt them to changes in the environment.

There indeed is a difference between the Darwinist/evolutionary geneticist point of view, and that of ID. And ID makes predictions. So, let's see if Daphnia is "susceptible" to these breaks, or, whether they use it as an adaptive strategy. It ought to be interesting.

"So, let me, from an ID perspective, predict something. I predict that it will be established that Daphnia, and related organism, USE double-stranded breaks, with the concomitant random generation of nucleotide strings, to overcome environmental challenges."

Wonderful, an ID prediction. Perhaps you didn't know that predictions should be derived logically from a clearly stated hypothesis, because I didn't see any ID hypothesis nor a derivation. I just see a prediction coming out of the blue. So let's try again. What specific ID hypothesis did you use to derive your prediction? Did you have to assume any constraints on the Designer's capabilities or goals? What ID assumptions are you operating on and how do you justify those assumptions?

Wonderful, an ID prediction. Perhaps you didn't know that predictions should be derived logically from a clearly stated hypothesis, because I didn't see any ID hypothesis nor a derivation. I just see a prediction coming out of the blue. So let's try again. What specific ID hypothesis did you use to derive your prediction? Did you have to assume any constraints on the Designer's capabilities or goals? What ID assumptions are you operating on and how do you justify those assumptions?

Lino already gave us the guiding principles of all ID 'research', remember?

Lino said...

T: "An unknown designer or designers at an unknown place and unknown time using unknown mechanisms and for unknown reasons designed some biological things"

This is not only plausible, it makes the most sense out of what we see.

If science discovers it, you can bet your last dollar that some IDiot somewhere will claim ID predicted it.

Wonderful, an ID prediction. Perhaps you didn't know that predictions should be derived logically from a clearly stated hypothesis, because I didn't see any ID hypothesis nor a derivation. I just see a prediction coming out of the blue. So let's try again. What specific ID hypothesis did you use to derive your prediction? Did you have to assume any constraints on the Designer's capabilities or goals? What ID assumptions are you operating on and how do you justify those assumptions?

The specific ID hypothesis is that the genome is "designed", thus inferring a Designer. Simple as that.

As to constraints, the constraints would be the same that any designer faces: economic utilization of resources, while providing every needed function.

As to assumptions, I assume that the Designer is logical, knowledgeable, and that the design strategy would be, as it is with humans, geared toward a definitive end.

My justification is simple: the genome has a logic that we recognize, and utilizes design strategies that we can also recognize--at least in part. This is just common sense.

Now: as Darwinists, what constraints are there to Darwinian evolution? And, what are your assumptions? And how do you justify them?

T: "An unknown designer or designers at an unknown place and unknown time using unknown mechanisms and for unknown reasons designed some biological things"

[This, is, of course, Thorton's deriding summary of what ID says.]

Still waiting for you to fill in the details. ANY details.

LDI: "This is not only plausible, it makes the most sense out of what we see."

Why don't you point out where my statement is wrong.

Not wrong per se, just meaningless, and completely worthless as a basis for scientific inquiry. But you IDiots aren't pushing your IDC crap because you want to advance scientific knowledge.

BTW, you still forgot to tell us why small local geologic catastrophes are a problem for evolution.

And, if it is your opinion that Darwinism is not only plausible, but makes the most sense out of what we see, then please describe how this is so.

Easy. ToE explains hundreds of years of empirical data from dozens of different scientific disciplines in a clear and consilient manner. It provides detailed mechanisms, a detailed timeline, and has made numerous predictions that have been demonstrated true.

While there are certainly still unknowns and areas of investigation, ToE is light years ahead of Intelligent Design Creationism. IDC has zero details, zero mechanisms, zero timeline, zero confirmed predictions. IDC is also not falsifiable.

troy: "What specific ID hypothesis did you use to derive your prediction? "

The specific ID hypothesis is that the genome is "designed", thus inferring a Designer. Simple as that.

Big time FAIL there poseur. You were asked for the specifics of your ID hypothesis that would lead you to the "double-stranded breaks, with the concomitant random generation of nucleotide strings" prediction.

Without a specific derivation to tie the prediction to your hypothesis, you may have well said "ID predicts the sun will rise tomorrow". Having the "prediction" be true won't be positive evidence for ID.

Dealing with you is like swatting away a gnat. Irritating at best. In fact, didn't they invent a word for you? I think it's called "troll".

Not wrong per se, just meaningless, and completely worthless as a basis for scientific inquiry.

You're fairly brilliant. At the same time as I've made a prediction based on ID principles, you make this statement. Do you ever think before you type?

ToE explains hundreds of years of empirical data from dozens of different scientific disciplines in a clear and consilient manner. It provides detailed mechanisms, a detailed timeline, and has made numerous predictions that have been demonstrated true.

Fairly pathetic. Give some details that can be refuted. Oh, wait a second. Darwinism is constructed from "just-so" stories, and so can't be refuted. You know, "just-so" stories---like the one you've just now given us.

This is as much as I will respond to you. Saynonara, my friend. I will dutifully ignore any and all of your comments in the future. I won't waste my time.

...and you're like scraping the dog crap off the bottom of one's shoe. Even when you're gone the stench remains.

At the same time as I've made a prediction based on ID principles

No poseur, you didn't. You made a "prediction" with no discernible connection to ID "principles." That's mainly because ID *has* no principles. Anything and everything that can possibly be found can be attributed to ID.

This is as much as I will respond to you.

You won't be the first cowardly Creationist to run from the evidence, and sadly you won't be the last. But that's OK. I'll stay here and point out your lies and stupidity regardless.

I responded to your post. Feduccia's 2007 paper should give any fair-minded person pause when it comes to the claims made by Xu and Cheng. It's a controverted area.

And, as I pointed out in my post, Archeopteryx, 10 million years prior to Sinosauropteryx, has modern (recent) bird feathers. So isn't it a little odd that it should be claimed that Sinosauropteryx is transitional in some way?

And, why is it that you care to discuss that here? What purpose does it serve? Are you a scoundrel too, like Thorton?

That is quite a charge, particularly given that, aside from the bluster, it misrepresents the OP. Nowhere do I say (nor did I say in the OP) that Lynch doubts evolution.

So what you're saying, basically, is that you quoted someone who totally accepts evolution in a post decrying it?

While, it's true, you didn't specifically make the claim that Mike Lynch denies evolution, Psi has a good point (and one which I've made countless times myself). Whenever you bring up 'latest research' which you think casts doubt on evolution, you are almost always quoting people who absolutely accept evolution - people who do not seem to think their own work contradicts it.

It should be at this point that you ask yourself whether you have fully understood the new findings. Because you rarely have.

It's one thing to quote someone and subject their words to critical analysis. It is quite another to quote someone in support of your point when they in fact do not support your point at all. It is tantamount to quote-mining.

Of course, the reason you do this is perfectly obvious. You like to cast the impression of 'evolutionists' being fringe fanatics, or otherwise a misguided subset of biologists. The actual fact is that the VAST majority of biologists are evolutionists - and those exceptionally rare ones that are not never actually seem to do any science. Whenever you say 'biologists' you are talking about 99.9% of biologists. You really might as well drop 'evolutionists' as a term and just use 'biologists' like everyone else. It is ID which is the fringe, religiously motivated, metaphysiscal, evidence-free pseudo-scientific movement.

And, as I pointed out in my post, Archeopteryx, 10 million years prior to Sinosauropteryx, has modern (recent) bird feathers. So isn't it a little odd that it should be claimed that Sinosauropteryx is transitional in some way?

All species are transitional. They are transitional between their ancestors and their descendants (unless they go extinct and fail to leave any descendants). That's kinda the point.

The relevance of Sinosauropteryx is to show there IS evidence of early 'proto-feathers'. They do not appear suddenly, complex and perfectly formed, as you seem to have been implying, presumably heading in the direction of a irriducible complexity argument.

As for the fact that Archaeopteryx predates Sinosauropteryx, so what? All that shows is that feathers probably evolved more than once. If you claimed there was no evidence of early transitional wings, I might in rebuttal point to the evidence of the bat's wing. It's true these weren't the FIRST wings, but so what? If bats can evolve wings, why can't birds? So it is with feathers.

"From the highlighted phrase in [4], it's clear you belong to the "neutral drift" crowd. So, then, it's no matter then that you throw Darwin over the side of the boat, as you do in the highlighted sentence from [2] above."

And:

"I'm afraid that without Darwin, you're assuming an evolutionary power without ever having demonstrated its power to exist. This, too, is problematic."

The thing is, Psi Wavefunction had already said this:

"But then again, adaptation is but one aspect of evolution, and in fact an emergent property of heritable variation and selection. Besides selection, there's also phenomena like drift and mutation that shape the ever-changing lifeforms."

You (lino) make it sound as though Psi Wavefunction relies ONLY on "neutral drift" to explain evolution and has completely discarded any ideas Darwin had, and any since the life of Darwin, but, as can be seen in all the comments from Psi Wavefunction (especially the ones above), that is clearly not the case.

Just because Psi Wavefunction said "few of us actually working in the field of evolutionary biology even care about Darwin's exact theory anymore" and "Doesn't matter whether he was right or wrong anymore...", doesn't mean that he has discarded all of Darwin's ideas.

The rest of Psi Wavefunction's comment...

"...,as the sheer vastness of knowledge accumulated on the subject far exceeds a single individual."

...should give you a big clue, as should some of the other things he said. What he's saying is that it doesn't really matter WHO came up with evolutionary theory ("except from a history of science perspective") and that it doesn't matter anymore whether Darwin himself was right or wrong about everything.

YOU, and other IDiots, are the ones who go on and on and on and on and on and on and on and on and on about Darwin, "Darwinism", "Darwinian", and "Darwinists". The ToE has moved on since Darwin, and that's the point. You and your fellow IDiots should try to accept the fact that it's almost 2012, and that a lot has been learned since 1859. Even more has been learned since the year zero, which is the year (and I'm being generous) that you religious wackos still live in mentally.

"But things aren't that simple are they?"

No, they aren't that simple. As I pointed out, Psi Wavefunction did not say that he relies only on neutral drift. Your very selective (and biased) reading of his words just makes you look, well, like an IDiot.

"If, as you say, selection is mostly stabilizing, then how is evolution driven forward?"

The answer is in your question, and it has to do with the word "mostly". Think about it.

Hint: If selection were ONLY and COMPLETELY stabilizing, you might have a point, but only regarding selection.

I want to add that I'm not necessarily comfortable with your term "driven forward".

First, thank you for the tone you've taken. It seems that you're interested in an exchange of ideas instead of nit-picking arguments here or there meant to promote oneself as having a real understanding when in fact you haven't.

All species are transitional. They are transitional between their ancestors and their descendants (unless they go extinct and fail to leave any descendants). That's kinda the point.

This is true if you accept: (1) common descent as direct descent, and (2) Darwinian theory.

To me, direct common descent doesn't really make any sense out of the fossil record as far as I can see, and the multiple times explosions of form that have occurred furthers the uneasiness. That puts me in the real minority when it comes to most ID people. But that's how I see it so far.

And, likewise, I cannot accept Darwinian theory because it appears to me to be too severely limited in its power to bring about changes to higher taxonomic forms.

Now, if the fossil record were to demonstrate lots of intermediate forms, then I would be inclined to think it plausible and permissible to assume that some kind(s) of genetic mechanism(s)truly exist, still undiscovered, that can explain macroevolutionary change through normal and natural random processes. But we don't see these intermediates either. So I'm disinclined.

So, since I neither subsribe to (1) or (2) above, your description of intermediates isn't anything I would accept as a given.

They do not appear suddenly, complex and perfectly formed, as you seem to have been implying, presumably heading in the direction of a irriducible complexity argument.

Yes, in a way that is where I was headed. But more along the lines that the time frame for development is, at a minimum, too short for Darwinian processes to fairly be assumed to have been at work.

. . . I might in rebuttal point to the evidence of the bat's wing. . . .

Well well, I see that gordon elliott mullings (GEM) did a drive by post, and instead of sticking around and facing challenges like a man, he just linked to garbage and ran away like the coward he is.

Hey gordo, just about all you, and a lot of other godbots, ever do is spew hate. Hate of and toward Darwin, "Darwinism", "Darwinists", atheists, evolutionists, evolutionary materialists, evolution, evolutionary theory, evolutionary biology, naturalists, scientists, science, agnostics, and a long list of others, including other religious people who have beliefs different than yours.

You try to play the victim and make it sound like you're being picked on for no good reason but what you conveniently ignore is that zealots like you have been dishing out hate (and war/genocide/threats/control/abuse/etc.) for thousands of years. You god zombies love to dish it out but you sure don't like it when your atrocious behavior is pointed out and when it's thrown back at you.

It seems that you're interested in an exchange of ideas instead of nit-picking arguments here or there meant to promote oneself as having a real understanding when in fact you haven't.

You mean exactly what you've been doing, trying to bluff your way through topics you don't understand.

R: "All species are transitional. They are transitional between their ancestors and their descendants (unless they go extinct and fail to leave any descendants). That's kinda the point."

This is true if you accept: (1) common descent as direct descent, and (2) Darwinian theory.

It's true even if you're a science denying IDiot. The facts don't change just because you refuse to accept them.

To me, direct common descent doesn't really make any sense out of the fossil record as far as I can see, and the multiple times explosions of form that have occurred furthers the uneasiness.

Ignorance based personal incredulity. Strike one.

And, likewise, I cannot accept Darwinian theory because it appears to me to be too severely limited in its power to bring about changes to higher taxonomic forms.

Ignorance based personal incredulity. Strike two.

Now, if the fossil record were to demonstrate lots of intermediate forms, then I would be inclined to think it plausible and permissible to assume that some kind(s) of genetic mechanism(s)truly exist, still undiscovered, that can explain macroevolutionary change through normal and natural random processes. But we don't see these intermediates either. So I'm disinclined.

Yes, we do see them. There are hundreds of well documented transitional sequences.

Why is an evolutionary a fact before an experiment and an assumption afterward?

Because religion drives science, and it matters™.

Stay tuned, during this 30-minute paid program Cornelius will explain us how to use the Abdomenizer and defeat materialistic rationalism. It will rock, rock, rock your way to a firmer stomach and the ultimate salvation.

To me, direct common descent doesn't really make any sense out of the fossil record as far as I can see.

Why not, in a nutshell?

And, likewise, I cannot accept Darwinian theory because it appears to me to be too severely limited in its power to bring about changes to higher taxonomic forms.

I'm going to need more clarification here. What higher taxonomic forms are you referring to and why would Darwinism be too limited to bring about changes to them?

Now, if the fossil record were to demonstrate lots of intermediate forms,

The fossil record does demonstrate lots of intermediate forms. To misquote myself, every species is intermediate between its ancestors and its descendants.

Yes, in a way that is where I was headed. But more along the lines that the time frame for development is, at a minimum, too short for Darwinian processes to fairly be assumed to have been at work.

Too short? What sort of time frame do you think we are working with here? It's not like we have a date when there were 'definitely no feathers in existence' and then a perfectly formed feather the very next year. Paleontology simply doesn't work like that. There is nothing at all stopping us assuming a 'development time' of 1, 2, or 10 million years from the earliest discovered feather.

Do you have a good reference for this?

I didn't. I was just plucking an example from off the top of my head. There are fossil bats, such as Onychonycteris finneyi and Icaronycteris, though...

Let me also take the opportunity to ask - you say you accept common ancestry between wolves, bears and even seals. What convinced you of this? Do you also accept common ancestry between all cats large and small, fossas, meerkats, mongooses and hyenas?

To me, direct common descent doesn't really make any sense out of the fossil record as far as I can see.

Why not, in a nutshell?

Most of the remarks and questions you ask get down to the following:

But more along the lines that the time frame for development is, at a minimum, too short for Darwinian processes to fairly be assumed to have been at work.

Too short? What sort of time frame do you think we are working with here? It's not like we have a date when there were 'definitely no feathers in existence' and then a perfectly formed feather the very next year. Paleontology simply doesn't work like that. There is nothing at all stopping us assuming a 'development time' of 1, 2, or 10 million years from the earliest discovered feather.

The problem is always one of a time frame. Positive selection takes a fair amount of time. Kimura, for example, in his book on neutral theory did a calculation for elephants, and, IIRC, came up with about six million years for a SNP at a specific locus. Fixation time for neutral drift is 1/4Ne, and for positive selection 1/2Nes. So, for positive selection maybe this happens a hundred times faster, or 60,000 years. But that's for only one SNP. For a series of ten SNP's, this ends up taking 600,000 years, and for one single de novoprotein, of average length 150 a.a., this would take 450 times 60,000 years, or 27 million years. It's calculations like these that create problems for my accepting Darwinian logic here. And I don't see how you can get around such problems.

Then, when you consider that the Cambrian Explosion took about 27 million years, how can you account for the appearance of 29 of the 30 future phyla all appearing in this relatively short period of time.

What I was suggesting was that if, in the Cambrian Explosion, we were to find all kinds of intermediate forms tracing their way from one precursor form, step-by-step, all the way to the newly arrived at phyla=bauplan, then this would be rather conclusive evidence that Darwinian processes, or, if you prefer, completely physico-chemical processes acting in a relatively random fashion, had the capacity of bringing about these new forms, and then it would simply be a matter of searching for the processes involved.

But this isn't what we have.

At UD, there's a link to a newly proposed mechanism called "plasticity-relaxation-mutation" (PRM) mechanism that the author believes superior to the strictly Darwinian (and Lamarckian) mechanism. It seems to me that it's this new way of thinking that will have to lead evolutionary biology forward. (This is not to say that PRM represents a method that is fully reducible to random physico-chemical processes, but, at least, it has a 'greater' explanatory power than meer Darwnism).

The problem is always one of a time frame. Positive selection takes a fair amount of time. Kimura, for example, in his book on neutral theory did a calculation for elephants, and, IIRC, came up with about six million years for a SNP at a specific locus. Fixation time for neutral drift is 1/4Ne, and for positive selection 1/2Nes. So, for positive selection maybe this happens a hundred times faster, or 60,000 years. But that's for only one SNP. For a series of ten SNP's, this ends up taking 600,000 years, and for one single de novoprotein, of average length 150 a.a., this would take 450 times 60,000 years, or 27 million years. It's calculations like these that create problems for my accepting Darwinian logic here. And I don't see how you can get around such problems.

Changes don't have to happen serially you moron. They can and do happen in parallel.

"At UD, there's a link to a newly proposed mechanism called "plasticity-relaxation-mutation" (PRM) mechanism that the author believes superior to the strictly Darwinian (and Lamarckian) mechanism."

Is the PRM not pretty much the same as the Facilitated variation proposed by Marc Kirschner and John Gerhart? Nonetheless I have no clue why IDiots are so horny about this stuff. It doesen´t to any harm to the theory of evolution and it does for sure make no case for IDC.

And by they why the fact that in the real scientific world additional/alternative explanations for the history of life are allowed (encouraged) to propose should by a clear case against all the darwinism-mafia nonsense spread by IDiots.

Maybe you should start to consider that the devastating failure of ID to gain ground in science is due to its failure to do science. Hey don´t worry at least you guys are quit successful to boost your nonsense for the religious crackpots.

Whether one thinks of them as "trolls" or as "gnats" (*), DarwinDefenders are pretty much interchangable ... and they seldom appear to be interested in reasoning. Consider this gem: "Maybe someone should ask Lino what's his ID explanation for Sinosauropteryx, Archaeopteryx, and the 10 million years time difference between their respective 'design' of feathers."

What our DarwinDefender fool is asserting is this: "Waaa! Unless you can give me a new 'explanation' that I will accept (that is, one that is grounded in materialism), then you have no right to point out the flaws in the 'explanation' I already assert (which is to say, one that is grounded in materialism)"

(*) Myself, I've settled on calling most of them "fools", as that nicely captures their intentional disinclination to reason.

illion, why are you avoiding my questions and questions from others? Are you afraid of the questions? Are you incapable of understanding the questions? Are you just another foolish cowardly IDiot who ignores and/or condemns anything that doesn't fit into your fairy tale religious beliefs?

Do you believe that a man can live inside a fish for three days and survive? Do you believe that a person can be turned in to a pillar of salt? Do you believe that a woman can be made from a man's rib? Do you believe that a man can come back to life after being dead for three days?

Since you're a christian, you must believe that stuff. Let's see you use 'reason' to explain those things and your belief in them. Then, let's see you reveal your 'reasoned' scientifically testable evidence and hypothesis that explains the diversity of life on Earth.

And while you're at it, let's see your 'reasoned' scientifically testable evidence and hypothesis for the existence of feathers and birds. (I would have said the 'evolution' of feathers and birds but understanding 'evolution' is obviously way beyond your capabilities)

By the way, were all but two penguins killed during 'the flood'? I can't find any reference to penguins in the bible. Maybe you can help me out and point to where they are mentioned?

Kimura, for example, in his book on neutral theory did a calculation for elephants, and, IIRC, came up with about six million years for a SNP at a specific locus.

For one thing, what is your starting point? If you are calculating the time it would take for an elephant to evolve, then the question is: evolve from what? From nothing? From a bacteria? From a small rodent-like mammal?

Secondly, as Thornton points out, it does sound like you are assuming these changes have to appear in a serial sequence. This, I think, is a mistake.

Also consider you are talking about the largest living land animal. True, there have once been bigger animals, but they really are the very tip of a gigantic iceberg. By far the majority of life on Earth is small - very small. Assuming everything on Earth would have the reproductive rate of an elephant would be like assuming every human in the world could run no faster than the least athletic 90-year-old you could find.

Then, when you consider that the Cambrian Explosion took about 27 million years, how can you account for the appearance of 29 of the 30 future phyla all appearing in this relatively short period of time.

A wonderful bit of spin there.

The phyla are vastly different now (made so by hundreds of millions of years genetic drift), but at the time of the Cambrian Explosion they were not. What have become, in modern species, enormous, clade-defining characteristics were once barely perceptible distinctions.

To demonstrate, look at this little worm-like chap:

http://paleobiology.si.edu/burgess/pikaia.html

This is Pikaia. Generally accepted as being the Cambrian's representative (or one of them, at least) of the Chordata phylum - that is, an ancestor of every single backboned animal: every fish, every amphibian, every reptile, every bird, and every mammal, all drawn from this one species, or something very much like it.

When we go back as far as the Cambrian Explosion (530 million years, give or take), the ancestors which were to give rise to the 29 future phylum all looked incredibly similar (mostly very small and simple work-like creatures).

What I was suggesting was that if, in the Cambrian Explosion, we were to find all kinds of intermediate forms tracing their way from one precursor form, step-by-step, all the way to the newly arrived at phyla=bauplan, then this would be rather conclusive evidence that Darwinian processes,

Why study a period that's so far back in the geological record? A time so far gone will inevitably be poorly populated with fossils. Why not observe this exact process in more modern animals where finding lots of 'intermediary' fossils is a more realistic goal?

Perhaps humans, for instance...?

At UD, there's a link to a newly proposed mechanism called "plasticity-relaxation-mutation" (PRM) mechanism that the author believes superior to the strictly Darwinian (and Lamarckian) mechanism.

I really don't think the paper says what you think it says. You do still realise this does nothing to further the case for ID/Creationism, right?

The phyla are vastly different now (made so by hundreds of millions of years genetic drift), but at the time of the Cambrian Explosion they were not. What have become, in modern species, enormous, clade-defining characteristics were once barely perceptible distinctions.

Ritchie, this is so ill-informed that there's no need to carry on the conversation any further.

Ilion:

What our DarwinDefender fool is asserting is this: "Waaa! Unless you can give me a new 'explanation' that I will accept (that is, one that is grounded in materialism), then you have no right to point out the flaws in the 'explanation' I already assert (which is to say, one that is grounded in materialism)"

The problem for them is that there is NO explanation that can be "grounded" in materialism. That is, there has yet to be any kind of postulated material causation that stands up to scrutiny. If they could do that, I wouldn't necessarily have a problem. But no such material mechanism exists. And, not only that, the problem---from a purely "materialistic" perspective---is so severe, that only the presence of some kind of super intelligent agency can possibly explain the complexity we see.

But were dealing with true believers.

(*) Myself, I've settled on calling most of them "fools", as that nicely captures their intentional disinclination to reason.

They appear to be scientific wannabe's. And, with evil intent. A rather pathetic combination.

Ritchie, this is so ill-informed that there's no need to carry on the conversation any further.

...and so Lino the poseur cuts and runs from yet another conversation where his dumb IDiot claims were successfully challenged. What's that make now Lino - seven, eight topics you've cowardly ducked out on? I've lost count.

I guess we'll never know how you determine complexity based on number of chromosomes, or know why small local catastrophes threaten ToE, or why you think genetic changes have to happen serially, or any of the other stupid claims you've made. Between you and Tedford and Ilion you're certainly doing the IDiot side proud!

The problem for them is that there is NO explanation that can be "grounded" in materialism.

Except the ones that have been empirically tested and verified with 150+ years worth of positive scientific evidence. But I suppose to you they don't count because they're not described by your GAWD in your Bible.

Your loss.

They appear to be scientific wannabe's. And, with evil intent. A rather pathetic combination.

Says the trolling ignoramus as he barfs up another bout of projection.

Ritchie, this is so ill-informed that there's no need to carry on the conversation any further.

If you think so then I am surprised you have decided to simply terminate the discussion rather than enlighten me. If you had evidence to support your point you could simply show it to me. Cutting and running smacks rather of a defense mechanism.

I guess we'll never know how you determine complexity based on number of chromosomes, or know why small local catastrophes threaten ToE, or why you think genetic changes have to happen serially, or any of the other stupid claims you've made. Between you and Tedford and Ilion you're certainly doing the IDiot side proud!

Lino, illion, tedford, and other IDiots, you'd be wise to pay close attention to this comment from Gary Gimbel:

"Maybe you should start to consider that the devastating failure of ID to gain ground in science is due to its failure to do science."

Wouldn't do any good. They couldn't care less if ID makes any scientific progress or not. ID isn't a scientific movement, it's a political movement designed to get their version of religious indoctrination forced into public schools. They know it, we know it, and after Dover most of the public knows it. As a result many if not most of the IDiots have dropped the bogus "ID isn't about religion!" claim.

"...only the presence of some kind of super intelligent agency can possibly explain the complexity we see."

Some kind? What kind exactly? Agency? What agency exactly? Your chosen god? Super? How "super"? How is super measured exactly? Complexity? How is complexity measured exactly? Presence? At what location is your alleged some kind of super intelligent agency present? Only? Can possibly explain? Can you support that with testable evidence?

Maybe I should point out that saying 'evolution sucks, therefor jesus' isn't evidence.

Cornelius G. Hunter is a graduate of the University of Illinois where
he earned a Ph.D. in Biophysics and Computational Biology. He is
Adjunct Professor at Biola University and author of the award-winning Darwin’s God: Evolution and the Problem of Evil. Hunter’s other books include Darwin’s Proof, and his newest book Science’s Blind Spot
(Baker/Brazos Press). Dr. Hunter's interest in the theory of evolution
involves the historical and theological, as well as scientific, aspects
of the theory. His website is http://www.darwins-god.blogspot.com/